I've always read that inline filters must either be in pressure fed fuel lines (not gravity fed) or if gravity fed, the fuel line diameter and the angle/ length-of-run of the fuel flow must allow sufficient fuel pressure/flow through the filter to prevent scavenging of air in the filter.
To address your second question, about servicing a bike that has been submerged... it is necessary to check for fluid contamination by water wherever fluid is maintained on the bike;
Rule #1 with any engine that is suspected to have been submerged, is NOT to crank the engine with the starter. Pull the spark plug, then crank to harmlessly expel water from the cylinder, otherwise serious damage may result.
Water in the cylinder will not compress thus forcing the crankshaft around with the starter motor may bend or break the connecting rod & or piston.
Many times people are lucky that their starter motor is not strong enough to crank the engine hard enough to do damage &/or most modern large single cylinder 4-stroke engines have a compression release that automatically engages when the starter motor is used.
The compression release opens the exhaust valve a little to make it easier to crank the engine, and thus will also inadvertently provide a path for water to be pushed out of the cylinder into the exhaust system.
Keep in mind that the exhaust system might also be full of water. The exhaust system must also be drained enough to allow air flow through the cylinder and out the exhaust valve before and engine will run.
You can also get hydro-lock in the crank case if water completely fills up the crank case in which case the piston cannot come down inside inside the crank case. The crank case would have to be drained enough to allow free movement of the piston and crankshaft.
The good news is that water is more dense than oil, therefore if allowed to sit for a short while, water and oil will separate. Water will settle to the bottom of the crank case while the oil will sit on top of the water. The crank case drain plug can be removed, long enough drain out water, then reinstalled when oil starts to drain out. Check the oil level to ensure the crank case is not overfilled. Drain more oil as necessary.
Of course the oil should be changed completely (multiple times) as soon as possible after it is contaminated. Thereafter the engine should be run at full operating temperature long enough to evaporate any remaining moisture in the crank case.
Water can gets into the following areas as well:
Gas tank- Generally speaking water tends to stay out of gas tanks, but water is more dense than gas, therefore if allowed to sit for a short while, water and gas will separate and the water can be drained out the petcock (remember to apply vacuum to vacuum operated petcocks to get them to flow)
float bowl- Carburetors will allow water in through the airbox/airfilter. Remove the air filter and wring the water it out if it is a foam type filter. Gauss type filters (K&N) just have to dry on their own enough to be used again. Paper air filters will not flow air once they get wet, even after they dry, and therefore must be replaced or the engine will not run. Also remove the drain screw in the carburetor float bowl, or remove the whole float bowl, to remove water. Blow air through the fuel line at the same time (by mouth, not compressed air) to push water out of the fuel line and carburetor.
Crank case- Crank cases will take on water through the PCV vent which is typically routed through the air box. Water may also get past the rings once inside the cylinder. Water gets into the cylinder by flowing through the carburetor or exhaust system into the cylinder via open valves, either intake or exhaust.
I hope this answers your question to some degree